Picard errors

[juliandwillett]

I have been getting errors through Picard where the script tries to run it as "picard" when for my server, it needs to be run as java -jar ../picard.jar. There does not seem to be a nice place to edit the code, any tips?

[juliandwillett]

I solved this on my computer cluster by manually downloading the version of picard cited in the paths.ini file. While there was later an error when the script tried to pass a "FU" parameter to the picard function, it bypassed the original error.